|
| Status |
Public on Oct 01, 2018 |
| Title |
marmoset_liver_adult_male2 |
| Sample type |
SRA |
| |
|
| Source name |
Adult liver
|
| Organism |
Callithrix jacchus |
| Characteristics |
tissue: liver
Sex: male
developmenta stage: adult
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
QIAGEN RNeasy Kit
Single-end strand-specific RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA LT kit according to manufacturer instructions. Libraries were sequenced using the Illumina HiSeq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
sample id: 5787sTS
|
| Data processing |
RNA-seq reads were aligned to the assembled genomes of their corresponding species using STAR (version 2.2.1) using the 2-pass mapping mode and standard settings.
Aligned reads from all replicates of each organ were used to reconstruct transcripts through a genome-guided de novo transcriptome assembly using StringTie (version 1.3.4d) with the following parameters: -j 5 –g 50.
Assembled transcripts from each organ were then merged using Cuffmerge to define a unique set of transcripts. Expression levels (measured in FPKM) of the assembled transcripts were calculated with Cuffnorm (version 2.2.1) with --library-norm-method classic-fpkm.
Genome_build: human: hg38; macaque: rheMac8; marmoset: calJac3; mouse: mm10; rat: rn6; rabbit: oryCun2
Supplementary_files_format_and_content: *sample_name*.Signal.UniqueMultiple.str*N*.out.bw: STAR-generated bigWig tracks of the RPM-normalized read coverage from each sample. Files represent reads mapped on the forward (N=1) or reverse (N=2) strand.
|
| |
|
| Submission date |
May 08, 2018 |
| Last update date |
Oct 01, 2018 |
| Contact name |
Francesco Nicola Carelli |
| E-mail(s) |
fr.carelli@gmail.com
|
| Organization name |
University of Cambridge
|
| Lab |
Julie Ahringer
|
| Street address |
Henry Wellcome Building of Cancer and Developmental Biology, Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21580 |
| Series (1) |
| GSE114191 |
Repurposing of promoters and enhancers during mammalian evolution |
|
| Relations |
| BioSample |
SAMN09093389 |
| SRA |
SRX4055836 |
